Conflicts between morphology-based taxonomy and mitochondrial phylogenies are a rampant phenomenon among cerithioidean freshwater gastropods, which is yet not completely understood. We have investigated snail populations sampled from several parts of the Moei River drainage in central Thailand that belong to a monophyletic mtDNA clade formally known as Brotia pagodula and recovered large degrees of variation in both the shell and mitochondrial sequences. When assessed independently, the levels of morphological and mitochondrial differentiation were indicative of the existence of more than one distinct species. Analyses of the shell resulted in the identification of two distinct morphotypes with a conical or elongate shape, respectively. Analyses of partial sequences of the mitochondrial genes 16S and COI revealed the existence of up to five well differentiated haplotype lineages. Rampant mismatch is observed when morphotypes are mapped onto the mtDNA phylogeny. Several explanations for this observation are discussed, such as the presence of paralogous sequences, incomplete lineage sorting of ancestral polymorphisms, presence of morphologically cryptic species and introgression of foreign haplotypes through hybridisation. The presence of nuclear gene copies of mitochondrial genes is refuted and incomplete lineage sorting at levels of up to 12% sequence divergence in COI in potentially panmictic populations is considered highly unlikely. We conclude that the discordance between morphologic and phylogenetic patterns are best explained by introgression of mtDNA haplotypes. Since Southeast Asian Pachychilidae are known to be poor dispersers and speciation is primarily thought to occur in allopatry, tectonic events and river captures during the Cenozoic are discussed as a potential factors mediating secondary contact between primarily allopatric sister species. We hypothesise that introgressive hybridisation between closely related species due to secondary contact has the potential to explain the mismatch between mitochondrial phylogenies and morphology-based species trees found in many groups of cerithioidean freshwater gastropods. This hypothesis requires further testing by future studies